Paper Citing NAMD - Abstract
Zanuy, David; Hamley, Ian W.; Aleman, Carlos
Modeling the Tetraphenylalanine-PEG Hybrid Amphiphile: From DFT Calculations on the Peptide to Molecular Dynamics Simulations on the Conjugate
JOURNAL OF PHYSICAL CHEMISTRY B, 115:8937-8946, JUL 21 2011
The conformational properties of the hybrid amphiphile formed by the conjugation of a hydrophobic peptide with four phenylalanine (Phe) residues and hydrophilic poly(ethylene glycol), have been investigated using quantum mechanical calculations and atomistic molecular dynamics simulations. The intrinsic conformational preferences of the peptide were examined using the building up search procedure combined with B3LYP/6-31G(d) geometry optimizations, which led to the identification of 78, 78, and 92 minimum energy structures for the peptides containing one, two, and four Phe residues. These peptides tend to adopt regular organizations involving turn-like motifs that define ribbon or helical-like arrangements. Furthermore, calculations indicate that backbone center dot center dot center dot side chain interactions involving the N-H of the amide groups and the pi clouds of the aromatic rings play a crucial role in Phe-containing peptides. On the other hand, MD simulations on the complete amphiphile in aqueous solution showed that the polymer fragment rapidly unfolds maximizing the contacts with the polar solvent, even though the hydrophobic peptide reduce the number of waters of hydration with respect to an individual polymer chain of equivalent molecular weight. In spite of the small effect of the peptide in the hydrodynamic properties of the polymer, we conclude that the two counterparts of the amphiphile tend to organize as independent modules.
